The Blue Earth River Watershed covers 1,550 square miles (992,034 acres) in south central Minnesota within the Minnesota River Basin. The Blue Earth River begins in northern Iowa and meets with the West Branch Blue Earth River in Faribault County. From there, it flows 108 miles northwardly in a winding course through eastern Faribault County into Blue Earth County, where it enters the Minnesota River. 

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The Blue Earth River (Dakota: Makhátho Wakpá) is the largest tributary by volume to the Minnesota River. It accounts for 46% of the Minnesota's flow at the rivers' confluence. It is a major contributor of sediment and nutrients to the Minnesota River.

 

​The watershed contains numerous rural cities including Fairmont, Jackson, Blue Earth, Wells, Winnebago, Vernon Center and part of the City of Mankato (see chart below). The watershed lies predominately in three counties: Blue Earth, Martin, Faribault, and a smaller portion in Freeborn County.